NM_004361.5:c.489C>T
Variant names:
Variant summary
Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2
The NM_004361.5(CDH7):c.489C>T(p.Pro163Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000932 in 1,609,534 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P163P) has been classified as Benign.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000096 ( 0 hom. )
Consequence
CDH7
NM_004361.5 synonymous
NM_004361.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -6.71
Publications
2 publications found
Genes affected
CDH7 (HGNC:1766): (cadherin 7) This gene encodes a type II classical cadherin of the cadherin superfamily. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature glycoprotein. This calcium dependent cell-cell adhesion molecule is comprised of five extracellular cadherin repeats, a transmembrane region and a highly conserved cytoplasmic tail. Type II (atypical) cadherins are defined based on their lack of a histidine-alanine-valine (HAV) cell adhesion recognition sequence specific to type I cadherins. Cadherins mediate cell-cell binding in a homophilic manner, contributing to the sorting of heterogeneous cell types. Mutations in this gene may be associated with bipolar disease in human patients. This gene is present in a gene cluster on chromosome 18. [provided by RefSeq, May 2016]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP7
Synonymous conserved (PhyloP=-6.71 with no splicing effect.
BS2
High AC in GnomAdExome4 at 14 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CDH7 | NM_004361.5 | c.489C>T | p.Pro163Pro | synonymous_variant | Exon 3 of 12 | ENST00000397968.4 | NP_004352.2 | |
| CDH7 | NM_001362438.2 | c.489C>T | p.Pro163Pro | synonymous_variant | Exon 3 of 12 | NP_001349367.1 | ||
| CDH7 | NM_033646.4 | c.489C>T | p.Pro163Pro | synonymous_variant | Exon 3 of 12 | NP_387450.1 | ||
| CDH7 | NM_001317214.3 | c.489C>T | p.Pro163Pro | synonymous_variant | Exon 3 of 11 | NP_001304143.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| CDH7 | ENST00000397968.4 | c.489C>T | p.Pro163Pro | synonymous_variant | Exon 3 of 12 | 1 | NM_004361.5 | ENSP00000381058.2 | ||
| CDH7 | ENST00000323011.7 | c.489C>T | p.Pro163Pro | synonymous_variant | Exon 3 of 12 | 1 | ENSP00000319166.3 | |||
| CDH7 | ENST00000536984.6 | c.489C>T | p.Pro163Pro | synonymous_variant | Exon 3 of 11 | 1 | ENSP00000443030.2 |
Frequencies
GnomAD3 genomes 0.00000659 AC: 1AN: 151716Hom.: 0 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
151716
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
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Gnomad ASJ
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Gnomad EAS
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Gnomad SAS
AF:
Gnomad FIN
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Gnomad MID
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Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.0000200 AC: 5AN: 249638 AF XY: 0.00000740 show subpopulations
GnomAD2 exomes
AF:
AC:
5
AN:
249638
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000960 AC: 14AN: 1457818Hom.: 0 Cov.: 32 AF XY: 0.00000552 AC XY: 4AN XY: 724310 show subpopulations
GnomAD4 exome
AF:
AC:
14
AN:
1457818
Hom.:
Cov.:
32
AF XY:
AC XY:
4
AN XY:
724310
show subpopulations
African (AFR)
AF:
AC:
1
AN:
33414
American (AMR)
AF:
AC:
4
AN:
44660
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26110
East Asian (EAS)
AF:
AC:
0
AN:
39584
South Asian (SAS)
AF:
AC:
0
AN:
86212
European-Finnish (FIN)
AF:
AC:
0
AN:
53392
Middle Eastern (MID)
AF:
AC:
0
AN:
5746
European-Non Finnish (NFE)
AF:
AC:
9
AN:
1108496
Other (OTH)
AF:
AC:
0
AN:
60204
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.493
Heterozygous variant carriers
0
1
2
4
5
6
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00000659 AC: 1AN: 151716Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74078 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
151716
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
74078
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41254
American (AMR)
AF:
AC:
0
AN:
15222
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3466
East Asian (EAS)
AF:
AC:
0
AN:
5148
South Asian (SAS)
AF:
AC:
0
AN:
4806
European-Finnish (FIN)
AF:
AC:
0
AN:
10530
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
1
AN:
67974
Other (OTH)
AF:
AC:
0
AN:
2088
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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